Changeset 3920

Timestamp:

May 31, 2020, 8:21:44 AM (3 years ago)

Author:

Peter

Message:

to handle ALT being <ID> string access to VCFHeader is needed and cannot be handled here. Instead we ignore those ALTs and documents the behaviour.

Location:

trunk/yat/omic

Files:

• VCF.cc (modified) (4 diffs)
• VCF.h (modified) (4 diffs)

trunk/yat/omic/VCF.cc

@@ -341 +341 @@
   {
     for (size_t i=0; i<vcf.alts().size(); ++i)
-      if (vcf.alts()[i].size() != vcf.ref().size())
+      if (vcf.alts()[i].size() != vcf.ref().size() &&
+          vcf.alts()[i][0]!='<')
         return true;
     return false;
@@ -349 +350 @@
   bool is_snv(const VCF& vcf)
   {
-    // FIXME we should handle the case when allele has format "<ID>"
     if (vcf.ref().size()!=1)
       return false;
@@ -363 +363 @@
   bool is_dnv(const VCF& vcf)
   {
-    // FIXME we should handle the case when allele has format "<ID>"
     if (vcf.ref().size()!=2)
       return false;
@@ -377 +376 @@
   bool is_mnv(const VCF& vcf)
   {
-    // FIXME we should handle the case when allele has format "<ID>"
     if (vcf.ref().size()<=2)
       return false;
 
     for (size_t i=0; i<vcf.alts().size(); ++i)
-      if (vcf.alts()[i].size()==vcf.ref().size())
+      if (vcf.alts()[i].size()==vcf.ref().size() &&
+          vcf.alts()[i][0]!='<')
         return true;
 

trunk/yat/omic/VCF.h

@@ -431 +431 @@
      \return true if at least one variant is an indel, i.e., if at
      least one alt allele is not the same size as ref.
+
+     \note ALT being an angle-bracketed ID string is ignored
    */
   bool is_indel(const VCF&);
@@ -437 +439 @@
      \return true if at least one variant is a single-nucleotide
      variant (SNV), i.e., ref is 1bp and at least one alt allele is
-     1bp.
+     1bp (but not '*').
+
+     \note ALT being an angle-bracketed ID string is ignored
    */
   bool is_snv(const VCF&);
@@ -445 +449 @@
      variant (DNV), i.e., ref is 2bp and at least one alt allele is
      2bp.
+
+     \note ALT being an angle-bracketed ID string is ignored
    */
   bool is_dnv(const VCF&);
@@ -452 +458 @@
      variant (MNV), i.e., ref is >2bp and at least one alt allele is
      same length as ref.
+
+     \note ALT being an angle-bracketed ID string is ignored
    */
   bool is_mnv(const VCF&);